1FYE

Aspartyl Dipeptidase (Anisotropic B-Factor Refinement)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of aspartyl dipeptidase reveals a unique fold with a Ser-His-Glu catalytic triad.

Hakansson, K.Wang, A.H.Miller, C.G.

(2000) Proc.Natl.Acad.Sci.USA 97: 14097-14102

  • DOI: 10.1073/pnas.260376797
  • Primary Citation of Related Structures:  1FY2

  • PubMed Abstract: 
  • The three-dimensional structure of Salmonella typhimurium aspartyl dipeptidase, peptidase E, was solved crystallographically and refined to 1.2-A resolution. The structure of this 25-kDa enzyme consists of two mixed beta-sheets forming a V, flanked b ...

    The three-dimensional structure of Salmonella typhimurium aspartyl dipeptidase, peptidase E, was solved crystallographically and refined to 1.2-A resolution. The structure of this 25-kDa enzyme consists of two mixed beta-sheets forming a V, flanked by six alpha-helices. The active site contains a Ser-His-Glu catalytic triad and is the first example of a serine peptidase/protease with a glutamate in the catalytic triad. The active site Ser is located on a strand-helix motif reminiscent of that found in alpha/beta-hydrolases, but the polypeptide fold and the organization of the catalytic triad differ from those of the known serine proteases. This enzyme is a member of a family of serine hydrolases and appears to represent a new example of convergent evolution of peptidase activity.


    Related Citations: 
    • Peptidase E, a peptidase specific for N-terminal aspartic dipeptides, is a serine hydrolase
      Lassy, R.A.,Miller, C.G.
      (2000) J.Bacteriol. 182: 2536
    • Cloning and nucleotide sequence of the cyclic AMP receptor protein-regulated Salmonella typhimurium pepE gene and crystallization of its product, an alpha-aspartyl dipeptidase
      Conlin, C.A.,Hakansson, K.,Liljas, A.,Miller, C.G.
      (1994) J.Bacteriol. 176: 166


    Organizational Affiliation

    Departments of Microbiology and Cell and Structural Biology, B103 Chemical and Life Science Laboratory, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, Urbana, IL 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ASPARTYL DIPEPTIDASE
A
229Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Gene Names: pepE
EC: 3.4.13.21
Find proteins for P36936 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P36936
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.986α = 90.00
b = 42.690β = 106.06
c = 62.496γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-10
    Type: Initial release
  • Version 1.1: 2007-10-21
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance